Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	4,356,671	T→G	15.8%	intergenic (‑81/+37)	dcuA ← / ← aspA	C4‑dicarboxylate antiporter/aspartate ammonia‑lyase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	4,356,671	0	T	G	15.8%	58.8 / 2.5	27	intergenic (‑81/+37)	dcuA/aspA	C4‑dicarboxylate antiporter/aspartate ammonia‑lyase
Reads supporting (aligned to +/- strand):  ref base T (18/4);  new base G (2/3);  total (20/7)
Fisher's exact test for biased strand distribution p-value = 9.13e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCCCAATCTGGCGCCCAAGAAGATCGCCAGCAAAACTATGATGAGTTCTACAACTAGCATATTAGCCTTCCTTGTTTTTTAACAAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACGTCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGTGCATCAGATTCTGTACGGAGAAAATATCGTCAAGTTCCGCTTCAGTCAA  >  CP009273/4356531‑4356803                                                                                                                                             |                                                                                                                                     ccccAATCTGGCGCCCAAGAAGATCGCCAGCAAAACTATGATGAGTTCTACAACTAGCATATTAGCCTTCCTTGTTTTTTAACAAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACGTCATCTGACGTg                                                                                                                              >  2:416710/1‑149 (MQ=255)           gcgcCCAAGAAGATCGCCAGCAAAACTATGATGAGTTCTACAACTACCATATTAGCCTTCCTTGTTTTTTAACAAGTTGATATTAGATTATTATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACGTCAGATGACGTGCCtt                                                                                                                          <  1:208872/143‑1 (MQ=255)             gcCCAAGAATATCGCCATCAAAACTATGATGAGTTCTACAACGAGCATATTAGCCTTCCTTGTTTTTTAACAAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACGTCATCTGACGTGCCtttt                                                                                                                        >  1:387141/1‑143 (MQ=255)                                 aaaCTATGATGAGTTCTACAACTAGCATATTAGCCTTCCTTGTTTTTTAACCAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGACAAAATGCACGTCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTAc                                                                                              >  2:166831/1‑149 (MQ=255)                                              ttCTACAACTAGCATATTAGCCTTCCTTGTTTTTTAACCAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACGTCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTccg                                                                                       >  1:308111/1‑141 (MQ=255)                                              ttCTACAACTAGCATATTAGCCTTCCTTGTTTTTTAACAAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACGTCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTCCTGTTCGCTTtcat                                                                                 >  2:95880/1‑149 (MQ=255)                                                      cTAGCATATTAGCCTTCCTTGTTTTTTAACAAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACGTCATCTGACGTGCCTTTTTTATTTGTACTCCCCTGTACGATTACTGTTCGCTTTCATCAGTATAg                                                                         >  2:39723/1‑149 (MQ=255)                                                             atTAGCCTTCCTTGTTTTTTAACAAGTTGGTATTAGATTGTTATTTTTAAGTTGCTGCTCACAAGAATAAAGGCACGTCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGCTCGCTTTCATGAGTATAGCGTTTTg                                                                  >  2:264555/1‑149 (MQ=255)                                                             atTAGCCTTCCTTGTTTTTTAACAAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACGTCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTg                                                                  >  2:80422/1‑149 (MQ=255)                                                                aGCCTTCCTTGTTTTTTAACAAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACGTCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTAAGATTACTGTTCGCTTTCATCGGTATGACGtt                                                                     >  1:77623/1‑143 (MQ=255)                                                                               ttAACAAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACGTCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCg                                                      <  1:266892/143‑1 (MQ=255)                                                                                  aCAAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACGTCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGTGCATCa                                             >  2:241325/1‑149 (MQ=255)                                                                                    aaGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACGTCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGGGc                                                 >  1:326894/1‑143 (MQ=255)                                                                                                 aTTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAAGCACGTCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCTTTTTGCTTTGTAAGCCGGGTGCATCAGATTCTGTa                                    >  1:238578/1‑143 (MQ=255)                                                                                                     ttATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACGTCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCTTTTTGCTTTGTAAGCCGGGTGCATCAGATTCTGTACGGAGaaatt                          >  2:425352/1‑147 (MQ=255)                                                                                                      tATTTTTAAGTTGCTGCTCACAAGAAAAAAGGCACGTCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGTGCATCAGATTCTGTAGGgag                               <  1:130569/143‑1 (MQ=255)                                                                                                         ttttAAGTTACGTCTCACAAGAAAAACGGCACGTCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGTGCACCAGATTCTGTACGGAGAAAATATCg                      <  2:218106/149‑1 (MQ=255)                                                                                                                    tGCTCACAAGAAAAAAGGCACGTCAGCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGGTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGTGCATCAGATTCTGTACGGAGAAAATATCGTCAAg                 <  1:339346/143‑1 (MQ=255)                                                                                                                      cTCACAAGAAAAAAGGCACGTCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGTGCATCAGATTCTGTACGGGGAAAATATCGTCAAGTTCCGCtt         >  2:76391/1‑149 (MQ=255)                                                                                                                      cTCACAAGAAAAAAGGCACGTCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGTGCATCAGATTCTGTACGGAGAAAATATCGTCAAGTTCCGCtt         >  2:148575/1‑149 (MQ=255)                                                                                                                      cTCACAAGAAAAAAGGCACGTCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGTGCATCAGATTCTGTACGGAGAAAATATCGTCAAGTTCCGCtt         >  2:76379/1‑149 (MQ=255)                                                                                                                          aaataaaaaaGGCACGTCAGATGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTGCTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGTGCATCCAATTCTGTACGGAGAAAGTATACTCAAGTTCCgg           >  1:170649/5‑142 (MQ=38)                                                                                                                           aaGAAAAAAGGCACGTCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGTGCATCAGATTCTGTACGGAGAAAATATCGTCAAGTTCCGCTTCAGTc    >  2:22684/1‑149 (MQ=255)                                                                                                                             gAAAAAAGGCACGTCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGTGCATCAGATTCTGTACGGAGAAAATATCGTCAAGTTCCGCTTc        >  1:113128/1‑143 (MQ=255)                                                                                                                             gAAAAAAGGCACGTCATCTGACGTGCCTTTTTTATTTGTACTAACCTTTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGTGCATCAGATTCTGTACGGAGAAAATATCGTCAAGTTCCGCTTc        <  1:373961/143‑1 (MQ=255)                                                                                                                              aaaaaaGGCACGTCAGCTGACGTGCCTTTTTTATTTGGACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGTGCATCAGATTCTGTACGGAGAAAATATCGTCAAGTTCCGCTTCa       <  1:97790/143‑1 (MQ=255)                                                                                                                                   aGGCACGTCAGATGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAGGCCGGGTGCAGCAGATTCTGTACGAGGAAAATCTAGGCACGTTCCGCTTCCGTCaa  >  1:3023/1‑143 (MQ=255)                                                                                                                                             |                                                                                                                                     CCCCAATCTGGCGCCCAAGAAGATCGCCAGCAAAACTATGATGAGTTCTACAACTAGCATATTAGCCTTCCTTGTTTTTTAACAAGTTGATATTAGATTGTTATTTTTAAGTTACTGCTCACAAGAAAAAAGGCACGTCATCTGACGTGCCTTTTTTATTTGTACTACCCTGTACGATTACTGTTCGCTTTCATCAGTATAGCGTTTTGCTTTGTAAGCCGGGTGCATCAGATTCTGTACGGAGAAAATATCGTCAAGTTCCGCTTCAGTCAA  >  CP009273/4356531‑4356803

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑